The US government rested its case against the WikiLeaks source, Bradley Manning on Tuesday, bringing to an end the prosecution phase of the most significant criminal trial of an official leaker in at least a generation.

In the course of more than four weeks of intermittent testimony, the prosecution has hit a number of legal hurdles, including conflicting testimony and paucity of concrete evidence. The most embarrassing admission was that the Army had mislaid the standard contract Manning signed that laid out the terms of his access to classified information upon deployment to Iraq.

In defence cross-examination of a prosecution witness, it was revealed that the government had lost one copy of the Acceptable Use Policy (AUP) that Manning had signed and had routinely burned a second copy filled out by the soldier and all other members of his unit. The document is important as it clarifies whether or not the soldier exceeded the terms of the authorised access to secret documents through his work computer that he directly agreed to.

Manning's lead defence lawyer, David Coombs, is likely to use the missing documents as grounds for having some of the charges dismissed. The AUP could be relevant to charges that Manning knowingly exceeded authorised access to a secret internet network, that he obtained classified information without authorisation and that he violated the computer fraud and abuse act.

To that end, prosecutors told the court that Manning's first transmission of classified information began within days or weeks of his arrival at Forward Operating Base Hammer, outside Baghdad, in November 2009. They tried to link Manning to a copy of a video of a US airstrike earlier that year, on the village of Garani in the Farah Province of Afghanistan, that was placed on to the computer of a systems administrator called Jason Katz at Brookhaven National Laboratory in Long Island in December.

But defence cross-examination of a key prosecution witness, special agent David Shaver, revealed that the Katz video did not match footage of the same Garani airstrike that was stored on Manning's workstation in Iraq. Manning indicated in earlier proceedings that he would admit to having leaked his copy of the Garani video in April 2010 – five months after he got to Iraq. But prosecutors refused to budge on their November 2009 timeframe, prompting Manning to plead not guilty to this count.

WikiLeaks founder Julian Assange at Ecuador's embassy in London, where he has been for almost a year. Photograph: Facundo Arrizabalaga/EPA

The government has also encountered problems seeking to prove that the army private entered into a conspiratorial relationship with Julian Assange and WikiLeaks. Prosecutors have pointed to the 2009 "Most Wanted List" compiled by WikiLeaks, which identified the most significant secrets that a crowd-sourced list of experts wanted to see disclosed. The government alleges that the list was used by Manning as a menu that guided his trawling of secure intelligence databases for information to leak. But no evidence was presented to court that Manning had ever read the list, let alone adopted it, and its status remains purely circumstantial.

Similarly, the prosecution cited a WikiLeaks tweet from May 2010, in which the anti-secrecy organisation put out an appeal to its Twitter followers for as many military email addresses to be leaked as possible. The government alleges a link between that tweet and a list of tens of thousands of email addresses that was found on Manning's personal computer. Yet the soldier never transmitted the list to WikiLeaks, and no evidence has been presented to court that he saw the WikiLeaks tweet in the first place.

The most serious charge, aiding the enemy, carries a maximum sentence of life in custody without parole. In pre-trial hearings the judge, Colonel Denise Lind, ruled that to make the charge stick the government must prove that Manning knowingly gave intelligence information, via WikiLeaks, to al-Qaida and its affiliates, including al-Qaida in the Arabian Peninsula. Crucially, Lind has set the prosecution the challenge of proving beyond a reasonable doubt that Manning had "a general evil intent", in that he "had to know he was dealing, directly or indirectly, with an enemy of the US". The soldier cannot be found guilty if he acted "inadvertently, accidentally, or negligently".

Whether or not the prosecution succeeds in meeting that high bar set by Lind will have far-reaching implications, not just for Manning, whose fate depends on it, but also for the wider relationship in the US between government, whistleblowers and a free press. The Obama administration has launched seven prosecutions under the Espionage Act, which Manning is also facing, more than double the number initiated by all previous presidents combined.

Manning has already pleaded guilty to lesser charges that carry a combined maximum sentence of 20 years. He has admitted to being the WikiLeaks source, and to acting in a way that was prejudicial to good order and discipline and that brought discredit upon the armed forces.

Such a substantial admission of responsibility has failed to satisfy military prosecutors, who are clearly determined to send a bold message that will give any would-be leaker pause. The aggression displayed by the US government has additional current significance given Edward Snowden's predicament as he attempts to avoid capture by US authorities to face Espionage Act charges for leaking National Security Agency state secrets.

Paradoxically, one of the most significant pieces of evidence presented by the prosecution to show that Manning had knowledge of the danger of his actions was a classified report that was among the trove he passed to WikiLeaks. The 32-page document was released by WikiLeaks in March 2010 and gave the conclusions of a major investigation by US counter-intelligence into WikiLeaks itself.

The government argues that having leaked the report, Manning must have been familiar with its content. The report states that WikiLeaks was a threat to the US army.

"The intentional or unintentional leaking and posting of US army sensitive or classified information to Wikileaks.org could result in increased threats to DoD personnel, equipment, facilities, or installations," the report said. "Such information could be of value to foreign intelligence and security services (FISS), foreign military forces, foreign insurgents, and foreign terrorist groups for collecting information or for planning attacks against US force, both within the United States and abroad."